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- EMDB-78042: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-78042
TitleBacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin, GerAB-focused
Map dataGerAB-focused reconstruction, full map sharpened
Sample
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
    • Protein or peptide: GerAA
    • Protein or peptide: GerAB
    • Protein or peptide: GerAC
Keywordschannel / amino acid / LeuT / SIGNALING PROTEIN
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsCofsky JC / Kruse AC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI164647 United States
Helen Hay Whitney Foundation United States
CitationJournal: To Be Published
Title: Bacterial spore nutrient receptors repurpose an ancient transporter as a germination trigger switch
Authors: Cofsky JC / Kruse AC
History
DepositionJul 11, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78042.png

Downloads & links

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Map

FileDownload / File: emd_78042.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGerAB-focused reconstruction, full map sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.7113068 - 1.2008246
Average (Standard dev.)0.00033795892 (±0.012029272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_78042_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: GerAB-focused reconstruction, full map unsharpened

Fileemd_78042_additional_1.map
AnnotationGerAB-focused reconstruction, full map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GerAB-focused reconstruction, half map 1

Fileemd_78042_half_map_1.map
AnnotationGerAB-focused reconstruction, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GerAB-focused reconstruction, half map 2

Fileemd_78042_half_map_2.map
AnnotationGerAB-focused reconstruction, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-...

EntireName: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
Components
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
    • Protein or peptide: GerAA
    • Protein or peptide: GerAB
    • Protein or peptide: GerAC

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Supramolecule #1: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-...

SupramoleculeName: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Macromolecule #1: GerAA

MacromoleculeName: GerAA / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 51.336789 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: DYKDDDDKGS LEVLFQGPGG SGSMEQTEFK EYIHDNLALV LPKLKENDDL VKNKKMLAN GLVFYYLYFS EMTDENKVSE AIKTLIKDEE TLTLDQVKKR L DQLDARPV ETAKKTIESI LNGNCAVFIN GLDKAYILTT GKKKTRSLTE PT TEKVVRG PKVAFVEDID ...String:
DYKDDDDKGS LEVLFQGPGG SGSMEQTEFK EYIHDNLALV LPKLKENDDL VKNKKMLAN GLVFYYLYFS EMTDENKVSE AIKTLIKDEE TLTLDQVKKR L DQLDARPV ETAKKTIESI LNGNCAVFIN GLDKAYILTT GKKKTRSLTE PT TEKVVRG PKVAFVEDID TNLALIRQRT SHPKLITKKI MIGENKLKPA AIM YIEGKA KKSVIKEVKA RLKNIQLEDI QDSGTLEELI EDNKYSPFPQ IQNT ERPDK VSSALFNGRV AILVDSSPFV LLVPVSLGIL MQSPDDYYER WISAS LIRS LRFASIFITL FLSSIYIALV SFHQGLLPTA LAVTISANRE NVPFPP IFE ALLMEVTIEL LREAGLRLPN PLGQTIGLVG GVVIGQAAVE ANLVSSI LV IVVSVIALAS FTVPQYGMGL SFRVLRFISM FSAAILGLYG IILFMLVV Y THLTRQTSFG SPYFSPNGFF SLKNTDDSII RLPIKNKPKE VNNPNEPKT DSTET

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Macromolecule #2: GerAB

MacromoleculeName: GerAB / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 40.086 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MSQKQTPLKL NTFQGISIVA NTMLGAGLLT LPRALTTKAN TPDGWITLIL EGFIFIFFI YLNTLIQKKH QYPSLFEYLK EGLGKWIGSI IGLLICGYFL G VASFETRA MAEMVKFFLL ERTPIQVIIL TFICCGIYLM VGGLSDVSRL FP FYLTVTI IILLIVFGIS ...String:
MSQKQTPLKL NTFQGISIVA NTMLGAGLLT LPRALTTKAN TPDGWITLIL EGFIFIFFI YLNTLIQKKH QYPSLFEYLK EGLGKWIGSI IGLLICGYFL G VASFETRA MAEMVKFFLL ERTPIQVIIL TFICCGIYLM VGGLSDVSRL FP FYLTVTI IILLIVFGIS FKIFDINNLR PVLGEGLGPI ANSLTVVSIS FLG MEVMLF LPEHMKKKKY TFRYASLGFL IPIILYILTY IIVVGALTAP EVKT LIWPT ISLFQSFELK GIFIERFESF LLVVWIIQFF TTFVIYGYFA ANGLK KTFG LSTKTSMVII GITVFYFSLW PDDANQVMMY SDYLGYIFVS LFLLPF ILF FIVALKRRIT TK

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Macromolecule #3: GerAC

MacromoleculeName: GerAC / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 853.9 Da
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: (LIG)CWDSENIEE LSLVIGIGLD KPDDENLELT QQIL VPKII SAKEGSSSDP TQLSITKGKT VHQMMRTSAL KHKPTFSQHL RLILL SKSV IADQIGMDAI INQFVRDNGT RRSSYVFITN GRTKDIFNMN DEGEPA SNV IYDLTENNKV TIRTMEPVTL GEISEHLTSD ...String:
(LIG)CWDSENIEE LSLVIGIGLD KPDDENLELT QQIL VPKII SAKEGSSSDP TQLSITKGKT VHQMMRTSAL KHKPTFSQHL RLILL SKSV IADQIGMDAI INQFVRDNGT RRSSYVFITN GRTKDIFNMN DEGEPA SNV IYDLTENNKV TIRTMEPVTL GEISEHLTSD DSFLIPHVGK ENGKLAI NG ASIIKNKLWH RDLTPIEVQN ISLFSGTVEG GVIDLKRDGH LFSYEVYS S NRKIKTAYKD GKFKFTVTRN IEGRLSEDWN PNEDSFKDSY IKSIEKTVE KRVHETVTSF ITEKLQKEIK ADVTGLGNEV RIHYPQKWKK ISRKWDDDYF SNAEIDYRV NVIVRDFGTK GANK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration11.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
Details: 15 mA, 30 s glow, 10 s hold, negative, easiGlow (Pelco)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: wait time = 10 s blot time = 6 s blot force above calibrated 0 = +23.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 9093 / Average exposure time: 2.52 sec. / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.6) / Number images used: 987106
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
FSC plot (resolution estimation)

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